Impact of the COVID-19 Pandemic on Antibiotic Resistant Infection Burden in U.S. Hospitals : Retrospective Cohort Study of Trends and Risk Factors

Abstract

Background: In 2022, the U.S. Centers for Disease Control and Prevention reported increases in antimicrobial resistance (AMR) across U.S. hospitals during the COVID-19 pandemic. The key drivers and lasting effects of this phenomenon remain unexplored.

Objective: To determine the incidence of AMR infections in U.S. hospitals during and beyond the pandemic and identify factors contributing to AMR.

Design: Retrospective cohort study.

Setting: 243 U.S. hospitals.

Participants: Adult hospitalizations, excluding inpatient transfers.

Intervention: Prepandemic (January 2018 to December 2019), peak pandemic (March 2020 to February 2022), and waning pandemic (March to December 2022).

Measurements: Incidence of methicillin-resistant Staphylococcus aureus; vancomycin-resistant Enterococci; extended-spectrum cephalosporin-resistant Enterobacterales; and carbapenem-resistant Enterobacterales, Acinetobacter baumannii, and Pseudomonas aeruginosa infections was evaluated among 120 continuously reporting hospitals. Infections detected more than 3 days after admission were classified as hospital-onset. Antibiotic exposure was estimated using a duration- and spectrum-weighted index. A competing risks analysis was done in 243 hospitals to identify risk factors for resistance.

Results: During the peak of the COVID-19 pandemic, AMR infections increased from 182 to 193 per 10 000 hospitalizations (6.5% [95% CI, 5.1% to 8.0%]). Hospital-onset AMR infections increased from 28.9 to 38.0 per 10 000 hospitalizations (31.5% [CI, 27.3% to 35.8%]). Factors associated with hospital-onset AMR included illness severity (intensive care unit admission, mechanical ventilation, vasopressors, COVID-19 diagnosis), comorbidities (Elixhauser Comorbidity Index), and prior exposure to antibiotics, but not hospital factors. Prevalence of AMR returned to prepandemic levels as the pandemic waned (182 to 182 per 10 000 hospitalizations; 0.4% [CI, -1.4% to 2.2%]), however, hospital-onset AMR remained above baseline (28.9 to 32.3 per 10 000 hospitalizations; 11.6% [CI, 6.8% to 16.7%]).

Limitation: Residual confounding; unknown appropriateness of antibiotics.

Conclusion: Sustained increases in hospital-onset AMR infections occurred in U.S. hospitals during the pandemic and were strongly associated with antibiotic exposure.

Primary funding source: National Institutes of Health Clinical Center; National Heart, Lung, and Blood Institute; and National Institute of Allergy and Infectious Diseases Intramural Research Programs.